"We are totally disappointed that the NFL and its leadership did not resolve the ongoing situation to the satisfaction of all parties long ago," CEO John Schnatter said in a call with investors on Wednesday. "This should have been nipped in the bud a year and a half ago."

"Leadership starts at the top, and this is an example of poor leadership," Schnatter said.

On Tuesday, Papa John's reported same-store sales grew 1% in the most recent quarter. The company additionally lowered it's North American same-store sales prediction for the year to 1.5%, down from 2 to 4%.

According to Papa John's, the chain's weaker-than-expected same-store sales can be blamed on the chain's association with the NFL following players' "polarizing" protests during the national anthem. Schnatter said that Papa John's is in contact with the league, making its concerns known.

"The controversy is polarizing the customer, polarizing the country," Schnatter said.

Papa John's CEO and founder John Schnatter Jason Merrit/Getty

This season, many players have knelt during the national anthem to protest racial inequality and police brutality.

Declining viewership isn't a new problem for the NFL, as ratings were down an average of 8% over the course of last season. Executives blamed last year's ratings drop — and corresponding Papa John's sales declines — on the election, saying that the company had expected an increase in ratings going into the 2017 season.

Papa John's executives said that while ratings declines certainly hurt Papa John's, the current negative association with the NFL is even more damaging. The company has even cut marketing that emphasizes the partnership, in an effort to avoid being associated with the league.

The NFL is crucial to Papa John's business. The company began its partnership with the NFL in 2010 and has "Preferred Pizza" partnerships with 23 NFL teams. Last year, the company signed a multi-year partnership with the NFL and the Super Bowl.

"Our partnership with the NFL, in particular, has been exceptional," Robert Thompson, senior vice president of marketing at Papa John's, told Business Insider in 2016. "One of the reasons the NFL is such a strong marketing opportunity is because of the number of people that watch the games live whether it be at home or in the stadium."